public static void WriteMzIdentMl(IEnumerable <PeptideSpectralMatch> psms, List <EngineLayer.ProteinGroup> groups, List <ModificationWithMass> variableMods, List <ModificationWithMass> fixedMods, List <Protease> proteases, double qValueFilter, Tolerance productTolerance, Tolerance parentTolerance, int missedCleavages, string outputPath)
{
psms = psms.Where(p => p.FdrInfo.QValue <= qValueFilter && p.FdrInfo.QValueNotch <= qValueFilter);
List <PeptideWithSetModifications> peptides = psms.SelectMany(i => i.CompactPeptides.SelectMany(c => c.Value.Item2)).Distinct().ToList();
List <Protein> proteins = peptides.Select(p => p.Protein).Distinct().ToList();
List <string> filenames = psms.Select(i => i.FullFilePath).Distinct().ToList();
Dictionary <string, string> database_reference = new Dictionary <string, string>();
List <string> databases = proteins.Select(p => p.DatabaseFilePath).Distinct().ToList();
UTF8Encoding utf8EmitBOM = new UTF8Encoding(false);
XmlWriterSettings settings = new XmlWriterSettings()
{
NewLineChars = "\n",
Indent = true,
Encoding = utf8EmitBOM,
};
XmlSerializer _indexedSerializer = new XmlSerializer(typeof(mzIdentML110.Generated.MzIdentMLType110));
var _mzid = new mzIdentML110.Generated.MzIdentMLType110()
{
version = "1.1.0",
id = "",
};
_mzid.Provider = new mzIdentML110.Generated.ProviderType()
{
id = "PROVIDER",
ContactRole = new mzIdentML110.Generated.ContactRoleType()
{
contact_ref = "UWMadisonSmithGroup",
Role = new mzIdentML110.Generated.RoleType()
{
cvParam = new mzIdentML110.Generated.CVParamType()
{
accession = "MS:1001271",
name = "researcher",
cvRef = "PSI-MS"
},
},
},
};
_mzid.AuditCollection = new mzIdentML110.Generated.AbstractContactType[2];
_mzid.AuditCollection[0] = new mzIdentML110.Generated.PersonType()
{
id = "UWMadisonSmithGroupPerson",
cvParam = new mzIdentML110.Generated.CVParamType[2]
{
new mzIdentML110.Generated.CVParamType()
{
accession = "MS:1000589",
name = "contact email",
cvRef = "PSI-MS",
value = "*****@*****.**"
},
new mzIdentML110.Generated.CVParamType()
{
accession = "MS:1000590",
name = "affiliation name",
cvRef = "PSI-MS",
value = "UWMadisonSmithGroup"
}
}
};
_mzid.AuditCollection[1] = new mzIdentML110.Generated.OrganizationType()
{
id = "UWMadisonSmithGroup",
cvParam = new mzIdentML110.Generated.CVParamType[2]
{
new mzIdentML110.Generated.CVParamType()
{
accession = "MS:1000589",
name = "contact email",
cvRef = "PSI-MS",
value = "*****@*****.**"
},
new mzIdentML110.Generated.CVParamType()
{
accession = "MS:1000590",
name = "affiliation name",
cvRef = "PSI-MS",
value = "UWMadisonSmithGroup"
}
}
};
//cvlist: URLs of controlled vocabularies used within the file.
_mzid.cvList = new mzIdentML110.Generated.cvType[4] {
new mzIdentML110.Generated.cvType()
{
id = "PSI-MS",
fullName = "Proteomics Standards Initiative Mass Spectrometry Vocabularies",
uri = "https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo",
version = "4.0.9"
},
new mzIdentML110.Generated.cvType()
{
id = "PSI-MOD",
fullName = "Proteomics Standards Initiative Modification Vocabularies",
uri = "http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mod/data/PSI-MOD.obo",
version = "1.2"
},
new mzIdentML110.Generated.cvType()
{
id = "UNIMOD",
fullName = "UNIT-ONTOLOGY",
uri = "http://www.unimod.org/obo/unimod.obo"
},
new mzIdentML110.Generated.cvType()
{
id = "UO",
fullName = "UNIT-ONTOLOGY",
uri = "http://www.unimod.org/obo/unimod.obo"
}
};
_mzid.AnalysisSoftwareList = new mzIdentML110.Generated.AnalysisSoftwareType[1] {
new mzIdentML110.Generated.AnalysisSoftwareType()
{
id = "AS_MetaMorpheus",
name = "MetaMorpheus",
version = GlobalVariables.MetaMorpheusVersion,
uri = "https://github.com/smith-chem-wisc/MetaMorpheus",
SoftwareName = new mzIdentML110.Generated.ParamType()
{
Item = new mzIdentML110.Generated.CVParamType
{
accession = "MS:1002826",
name = "MetaMorpheus",
cvRef = "PSI-MS"
}
},
ContactRole = new mzIdentML110.Generated.ContactRoleType()
{
contact_ref = "UWMadisonSmithGroup",
Role = new mzIdentML110.Generated.RoleType()
{
cvParam = new mzIdentML110.Generated.CVParamType()
{
accession = "MS:1001267",
name = "software vendor",
cvRef = "PSI-MS"
}
}
}
}
};
_mzid.DataCollection = new mzIdentML110.Generated.DataCollectionType
{
AnalysisData = new mzIdentML110.Generated.AnalysisDataType()
{
SpectrumIdentificationList = new mzIdentML110.Generated.SpectrumIdentificationListType[1]
{
new mzIdentML110.Generated.SpectrumIdentificationListType
{
id = "SIL",
SpectrumIdentificationResult = new mzIdentML110.Generated.SpectrumIdentificationResultType[psms.Count()]
}
}
},
Inputs = new mzIdentML110.Generated.InputsType
{
SearchDatabase = new mzIdentML110.Generated.SearchDatabaseType[databases.Count()],
SpectraData = new mzIdentML110.Generated.SpectraDataType[filenames.Count]
}
};
_mzid.SequenceCollection = new mzIdentML110.Generated.SequenceCollectionType
{
Peptide = new mzIdentML110.Generated.PeptideType[peptides.Count],
DBSequence = new mzIdentML110.Generated.DBSequenceType[proteins.Count],
PeptideEvidence = new mzIdentML110.Generated.PeptideEvidenceType[peptides.Count]
};
_mzid.AnalysisCollection = new mzIdentML110.Generated.AnalysisCollectionType
{
SpectrumIdentification = new mzIdentML110.Generated.SpectrumIdentificationType[1]
{
new mzIdentML110.Generated.SpectrumIdentificationType
{
id = "SI",
spectrumIdentificationList_ref = "SIL",
spectrumIdentificationProtocol_ref = "SIP",
InputSpectra = new mzIdentML110.Generated.InputSpectraType[filenames.Count],
SearchDatabaseRef = new mzIdentML110.Generated.SearchDatabaseRefType[databases.Count]
}
}
};
int database_index = 0;
foreach (string database in databases)
{
_mzid.DataCollection.Inputs.SearchDatabase[database_index] = new mzIdentML110.Generated.SearchDatabaseType()
{
id = "SDB_" + database_index,
location = database,
DatabaseName = new mzIdentML110.Generated.ParamType
{
Item = new mzIdentML110.Generated.CVParamType
{
accession = "MS:1001073",
name = "database type amino acid",
cvRef = "PSI-MS"
}
}
};
database_reference.Add(database, "SDB_" + database_index);
_mzid.AnalysisCollection.SpectrumIdentification[0].SearchDatabaseRef[database_index] = new mzIdentML110.Generated.SearchDatabaseRefType()
{
searchDatabase_ref = "SDB_" + database_index
};
database_index++;
}
int protein_index = 0;
foreach (Protein protein in proteins)
{
_mzid.SequenceCollection.DBSequence[protein_index] = new mzIdentML110.Generated.DBSequenceType
{
id = "DBS_" + protein.Accession,
lengthSpecified = true,
length = protein.Length,
searchDatabase_ref = database_reference[protein.DatabaseFilePath],
accession = protein.Accession,
Seq = protein.BaseSequence,
cvParam = new mzIdentML110.Generated.CVParamType[1]
{
new mzIdentML110.Generated.CVParamType
{
accession = "MS:1001088",
name = "protein description",
cvRef = "PSI-MS",
value = protein.FullDescription
}
},
name = protein.Name
};
protein_index++;
}
Dictionary <string, int> spectral_ids = new Dictionary <string, int>(); //key is datafile, value is datafile's id
int spectra_data_id = 0;
foreach (string data_filepath in filenames)
{
bool thermoRawFile = Path.GetExtension(data_filepath) == ".raw";
string spectral_data_id = "SD_" + spectra_data_id;
spectral_ids.Add(data_filepath, spectra_data_id);
_mzid.AnalysisCollection.SpectrumIdentification[0].InputSpectra[spectra_data_id] = new mzIdentML110.Generated.InputSpectraType()
{
spectraData_ref = spectral_data_id
};
_mzid.DataCollection.Inputs.SpectraData[spectra_data_id] = new mzIdentML110.Generated.SpectraDataType()
{
id = spectral_data_id,
name = Path.GetFileNameWithoutExtension(data_filepath),
location = data_filepath,
FileFormat = new mzIdentML110.Generated.FileFormatType
{
cvParam = new mzIdentML110.Generated.CVParamType
{
accession = thermoRawFile ? "MS:1000563" : "MS:1000584",
name = thermoRawFile ? "Thermo RAW format" : "mzML format",
cvRef = "PSI-MS"
}
},
SpectrumIDFormat = new mzIdentML110.Generated.SpectrumIDFormatType
{
cvParam = new mzIdentML110.Generated.CVParamType
{
accession = thermoRawFile ? "MS:1000768" : "MS:1001530",
name = thermoRawFile ? "Thermo nativeID format" : "mzML unique identifier",
cvRef = "PSI-MS"
}
}
};
spectra_data_id++;
}
int sir_id = 0;
int pe_index = 0;
int p_index = 0;
Dictionary <PeptideWithSetModifications, int> peptide_evidence_ids = new Dictionary <PeptideWithSetModifications, int>();
Dictionary <string, Tuple <int, HashSet <string> > > peptide_ids = new Dictionary <string, Tuple <int, HashSet <string> > >(); //key is peptide sequence, value is <peptide id for that peptide, peptide evidences>, list of spectra id's
Dictionary <Tuple <string, int>, Tuple <int, int> > psm_per_scan = new Dictionary <Tuple <string, int>, Tuple <int, int> >(); //key is <filename, scan numer> value is <scan result id, scan item id #'s (could be more than one ID per scan)>
var unambiguousPsms = psms.Where(psm => psm.FullSequence != null);
foreach (PeptideSpectralMatch psm in unambiguousPsms)
{
foreach (PeptideWithSetModifications peptide in psm.CompactPeptides.SelectMany(c => c.Value.Item2).Distinct())
{
//if first peptide on list hasn't been added, add peptide and peptide evidence
if (!peptide_ids.TryGetValue(peptide.Sequence, out Tuple <int, HashSet <string> > peptide_id))
{
peptide_id = new Tuple <int, HashSet <string> >(p_index, new HashSet <string>());
p_index++;
_mzid.SequenceCollection.Peptide[peptide_id.Item1] = new mzIdentML110.Generated.PeptideType
{
PeptideSequence = peptide.BaseSequence,
id = "P_" + peptide_id.Item1,
Modification = new mzIdentML110.Generated.ModificationType[peptide.NumMods]
};
int mod_id = 0;
foreach (KeyValuePair <int, ModificationWithMass> mod in peptide.AllModsOneIsNterminus)
{
_mzid.SequenceCollection.Peptide[peptide_id.Item1].Modification[mod_id] = new mzIdentML110.Generated.ModificationType()
{
location = mod.Key - 1,
locationSpecified = true,
monoisotopicMassDelta = mod.Value.monoisotopicMass,
residues = new string[1] {
peptide.BaseSequence[Math.Min(Math.Max(0, mod.Key - 2), peptide.Length - 1)].ToString()
},
monoisotopicMassDeltaSpecified = true,
cvParam = new mzIdentML110.Generated.CVParamType[1]
{
GetUnimodCvParam(mod.Value)
}
};
mod_id++;
}
peptide_ids.Add(peptide.Sequence, peptide_id);
}
if (!peptide_evidence_ids.ContainsKey(peptide))
{
_mzid.SequenceCollection.PeptideEvidence[pe_index] = new mzIdentML110.Generated.PeptideEvidenceType()
{
id = "PE_" + pe_index,
peptide_ref = "P_" + peptide_id.Item1,
dBSequence_ref = "DBS_" + peptide.Protein.Accession,
isDecoy = peptide.Protein.IsDecoy,
startSpecified = true,
start = peptide.OneBasedStartResidueInProtein,
endSpecified = true,
end = peptide.OneBasedEndResidueInProtein,
pre = peptide.PreviousAminoAcid.ToString(),
post = (peptide.OneBasedEndResidueInProtein < peptide.Protein.BaseSequence.Length) ? peptide.Protein[peptide.OneBasedEndResidueInProtein].ToString() : "-",
};
peptide_evidence_ids.Add(peptide, pe_index);
pe_index++;
}
}
if (!psm_per_scan.TryGetValue(new Tuple <string, int>(psm.FullFilePath, psm.ScanNumber), out Tuple <int, int> scan_result_scan_item)) //check to see if scan has already been added
{
scan_result_scan_item = new Tuple <int, int>(sir_id, 0);
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[scan_result_scan_item.Item1] = new mzIdentML110.Generated.SpectrumIdentificationResultType()
{
id = "SIR_" + scan_result_scan_item.Item1,
spectraData_ref = "SD_" + spectral_ids[psm.FullFilePath].ToString(),
spectrumID = "scan=" + psm.ScanNumber.ToString(),
SpectrumIdentificationItem = new mzIdentML110.Generated.SpectrumIdentificationItemType[500],
cvParam = new mzIdentML110.Generated.CVParamType[1]
{
new mzIdentML110.Generated.CVParamType
{
name = "scan start time",
cvRef = "PSI-MS",
accession = "MS:1000016",
value = psm.ScanRetentionTime.ToString()
}
}
};
psm_per_scan.Add(new Tuple <string, int>(psm.FullFilePath, psm.ScanNumber), scan_result_scan_item);
sir_id++;
}
else
{
psm_per_scan[new Tuple <string, int>(psm.FullFilePath, psm.ScanNumber)] = new Tuple <int, int>(scan_result_scan_item.Item1, scan_result_scan_item.Item2 + 1);
scan_result_scan_item = psm_per_scan[new Tuple <string, int>(psm.FullFilePath, psm.ScanNumber)];
}
foreach (PeptideWithSetModifications p in psm.CompactPeptides.SelectMany(c => c.Value.Item2).Distinct())
{
peptide_ids[p.Sequence].Item2.Add("SII_" + scan_result_scan_item.Item1 + "_" + scan_result_scan_item.Item2);
}
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[scan_result_scan_item.Item1].SpectrumIdentificationItem[scan_result_scan_item.Item2] = new mzIdentML110.Generated.SpectrumIdentificationItemType()
{
rank = 1,
chargeState = psm.ScanPrecursorCharge,
id = "SII_" + scan_result_scan_item.Item1 + "_" + scan_result_scan_item.Item2,
experimentalMassToCharge = Math.Round(psm.ScanPrecursorMonoisotopicPeakMz, 5),
passThreshold = psm.FdrInfo.QValue <= 0.01,
//NOTE:ONLY CAN HAVE ONE PEPTIDE REF PER SPECTRUM IDENTIFICATION ITEM
peptide_ref = "P_" + peptide_ids[psm.FullSequence].Item1,
PeptideEvidenceRef = new mzIdentML110.Generated.PeptideEvidenceRefType[psm.CompactPeptides.SelectMany(c => c.Value.Item2).Distinct().Count()],
cvParam = new mzIdentML110.Generated.CVParamType[2]
{
new mzIdentML110.Generated.CVParamType
{
name = "MetaMorpheus:score",
cvRef = "PSI-MS",
accession = "MS:1002827",
value = psm.Score.ToString()
},
new mzIdentML110.Generated.CVParamType
{
accession = "MS:1002354",
name = "PSM-level q-value",
cvRef = "PSI-MS",
value = psm.FdrInfo.QValue.ToString()
}
}
};
if (psm.PeptideMonisotopicMass.HasValue)
{
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[scan_result_scan_item.Item1].SpectrumIdentificationItem[scan_result_scan_item.Item2].calculatedMassToCharge = Math.Round(psm.PeptideMonisotopicMass.Value.ToMz(psm.ScanPrecursorCharge), 5);
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[scan_result_scan_item.Item1].SpectrumIdentificationItem[scan_result_scan_item.Item2].calculatedMassToChargeSpecified = true;
}
int pe = 0;
foreach (PeptideWithSetModifications p in psm.CompactPeptides.SelectMany(c => c.Value.Item2).Distinct())
{
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[scan_result_scan_item.Item1].SpectrumIdentificationItem[scan_result_scan_item.Item2].PeptideEvidenceRef[pe]
= new mzIdentML110.Generated.PeptideEvidenceRefType
{
peptideEvidence_ref = "PE_" + peptide_evidence_ids[p]
};
pe++;
}
}
_mzid.AnalysisProtocolCollection = new mzIdentML110.Generated.AnalysisProtocolCollectionType()
{
SpectrumIdentificationProtocol = new mzIdentML110.Generated.SpectrumIdentificationProtocolType[1]
{
new mzIdentML110.Generated.SpectrumIdentificationProtocolType
{
id = "SIP",
analysisSoftware_ref = "AS_MetaMorpheus",
SearchType = new mzIdentML110.Generated.ParamType
{
Item = new mzIdentML110.Generated.CVParamType
{
accession = "MS:1001083",
name = "ms-ms search",
cvRef = "PSI-MS"
}
},
AdditionalSearchParams = new mzIdentML110.Generated.ParamListType()
{
//TODO: ADD SEARCH PARAMS?
Items = new mzIdentML110.Generated.AbstractParamType[2]
{
new mzIdentML110.Generated.CVParamType
{
accession = "MS:1001211",
cvRef = "PSI-MS",
name = "parent mass type mono"
},
new mzIdentML110.Generated.CVParamType
{
accession = "MS:1001255",
name = "fragment mass type mono",
cvRef = "PSI-MS"
},
}
},
ModificationParams = new mzIdentML110.Generated.SearchModificationType[fixedMods.Count + variableMods.Count],
Enzymes = new mzIdentML110.Generated.EnzymesType()
{
Enzyme = new mzIdentML110.Generated.EnzymeType[proteases.Count]
},
FragmentTolerance = new mzIdentML110.Generated.CVParamType[2]
{
new mzIdentML110.Generated.CVParamType
{
accession = "MS:1001412",
name = "search tolerance plus value",
value = productTolerance.Value.ToString(),
cvRef = "PSI-MS",
unitAccession = productTolerance is PpmTolerance? "UO:0000169": "UO:0000221",
unitName = productTolerance is PpmTolerance? "parts per million" : "dalton",
unitCvRef = "UO"
},
new mzIdentML110.Generated.CVParamType
{
accession = "MS:1001413",
name = "search tolerance minus value",
value = productTolerance.Value.ToString(),
cvRef = "PSI-MS",
unitAccession = productTolerance is PpmTolerance? "UO:0000169": "UO:0000221",
unitName = productTolerance is PpmTolerance? "parts per million" : "dalton",
unitCvRef = "UO"
}
},
ParentTolerance = new mzIdentML110.Generated.CVParamType[2]
{
new mzIdentML110.Generated.CVParamType
{
accession = "MS:1001412",
name = "search tolerance plus value",
value = parentTolerance.Value.ToString(),
cvRef = "PSI-MS",
unitAccession = parentTolerance is PpmTolerance? "UO:0000169": "UO:0000221",
unitName = parentTolerance is PpmTolerance? "parts per million" : "dalton",
unitCvRef = "UO"
},
new mzIdentML110.Generated.CVParamType
{
accession = "MS:1001413",
name = "search tolerance minus value",
value = parentTolerance.Value.ToString(),
cvRef = "PSI-MS",
unitAccession = parentTolerance is PpmTolerance? "UO:0000169": "UO:0000221",
unitName = parentTolerance is PpmTolerance? "parts per million" : "dalton",
unitCvRef = "UO"
}
},
Threshold = new mzIdentML110.Generated.ParamListType()
{
Items = new mzIdentML110.Generated.CVParamType[1]
{
new mzIdentML110.Generated.CVParamType
{
accession = "MS:1001448",
name = "pep:FDR threshold",
cvRef = "PSI-MS",
value = "0.01"
}
}
}
}
}
};
int protease_index = 0;
foreach (Protease protease in proteases)
{
_mzid.AnalysisProtocolCollection.SpectrumIdentificationProtocol[0].Enzymes.Enzyme[protease_index] = new mzIdentML110.Generated.EnzymeType()
{
id = "E_" + protease_index,
name = protease.Name,
semiSpecific = protease.CleavageSpecificity == CleavageSpecificity.Semi,
missedCleavagesSpecified = true,
missedCleavages = missedCleavages,
SiteRegexp = protease.SiteRegexp,
EnzymeName = new mzIdentML110.Generated.ParamListType()
{
Items = new mzIdentML110.Generated.AbstractParamType[1]
{
new mzIdentML110.Generated.CVParamType
{
accession = protease.PsiMsAccessionNumber,
name = protease.PsiMsName,
cvRef = "PSI-MS"
}
}
}
};
protease_index++;
}
int mod_index = 0;
foreach (ModificationWithMass mod in fixedMods)
{
_mzid.AnalysisProtocolCollection.SpectrumIdentificationProtocol[0].ModificationParams[mod_index] = new mzIdentML110.Generated.SearchModificationType()
{
fixedMod = true,
massDelta = (float)mod.monoisotopicMass,
residues = mod.motif.ToString(),
cvParam = new mzIdentML110.Generated.CVParamType[1]
{
GetUnimodCvParam(mod)
}
};
mod_index++;
}
foreach (ModificationWithMass mod in variableMods)
{
_mzid.AnalysisProtocolCollection.SpectrumIdentificationProtocol[0].ModificationParams[mod_index] = new mzIdentML110.Generated.SearchModificationType()
{
fixedMod = false,
massDelta = (float)mod.monoisotopicMass,
residues = mod.motif.ToString(),
cvParam = new mzIdentML110.Generated.CVParamType[1]
{
GetUnimodCvParam(mod)
}
};
mod_index++;
}
_mzid.AnalysisProtocolCollection.ProteinDetectionProtocol = new mzIdentML110.Generated.ProteinDetectionProtocolType()
{
id = "PDP",
analysisSoftware_ref = "AS_MetaMorpheus",
Threshold = new mzIdentML110.Generated.ParamListType()
{
Items = new mzIdentML110.Generated.CVParamType[1]
{
new mzIdentML110.Generated.CVParamType
{
accession = "MS:1001447",
name = "prot:FDR threshold",
cvRef = "PSI-MS",
value = "0.01"
}
}
}
};
if (groups != null)
{
_mzid.DataCollection.AnalysisData.ProteinDetectionList = new mzIdentML110.Generated.ProteinDetectionListType()
{
id = "PDL",
ProteinAmbiguityGroup = new mzIdentML110.Generated.ProteinAmbiguityGroupType[groups.Count]
};
int group_id = 0;
int protein_id = 0;
foreach (EngineLayer.ProteinGroup proteinGroup in groups)
{
_mzid.DataCollection.AnalysisData.ProteinDetectionList.ProteinAmbiguityGroup[group_id] = new mzIdentML110.Generated.ProteinAmbiguityGroupType()
{
id = "PAG_" + group_id,
ProteinDetectionHypothesis = new mzIdentML110.Generated.ProteinDetectionHypothesisType[proteinGroup.Proteins.Count]
};
int pag_protein_index = 0;
foreach (Protein protein in proteinGroup.Proteins)
{
_mzid.DataCollection.AnalysisData.ProteinDetectionList.ProteinAmbiguityGroup[group_id].ProteinDetectionHypothesis[pag_protein_index] = new mzIdentML110.Generated.ProteinDetectionHypothesisType()
{
id = "PDH_" + protein_id,
dBSequence_ref = "DBS_" + protein.Accession,
passThreshold = proteinGroup.QValue <= 0.01, // hardcoded as 1% FDR but we could change this to the provided threshold
PeptideHypothesis = new mzIdentML110.Generated.PeptideHypothesisType[proteinGroup.AllPeptides.Count],
cvParam = new mzIdentML110.Generated.CVParamType[4]
{
new mzIdentML110.Generated.CVParamType
{
accession = "MS:1002828",
name = "MetaMorpheus:protein score",
cvRef = "PSI-MS",
value = proteinGroup.ProteinGroupScore.ToString()
},
new mzIdentML110.Generated.CVParamType
{
accession = "MS:1002373",
name = "protein group-level q-value",
cvRef = "PSI-MS",
value = proteinGroup.QValue.ToString()
},
new mzIdentML110.Generated.CVParamType
{
accession = "MS:1001093",
name = "sequence coverage",
cvRef = "PSI-MS",
value = proteinGroup.SequenceCoveragePercent.First().ToString()
},
new mzIdentML110.Generated.CVParamType
{
accession = "MS:1001097",
name = "distinct peptide sequences",
cvRef = "PSI-MS",
value = proteinGroup.UniquePeptides.Count.ToString()
}
}
};
int peptide_id = 0;
foreach (PeptideWithSetModifications peptide in proteinGroup.AllPeptides)
{
if (peptide_evidence_ids.ContainsKey(peptide))
{
if (peptide.Protein == protein)
{
_mzid.DataCollection.AnalysisData.ProteinDetectionList.ProteinAmbiguityGroup[group_id].ProteinDetectionHypothesis[pag_protein_index].PeptideHypothesis[peptide_id] = new mzIdentML110.Generated.PeptideHypothesisType()
{
peptideEvidence_ref = "PE_" + peptide_evidence_ids[peptide],
SpectrumIdentificationItemRef = new mzIdentML110.Generated.SpectrumIdentificationItemRefType[peptide_ids[peptide.Sequence].Item2.Count],
};
int i = 0;
foreach (string sii in peptide_ids[peptide.Sequence].Item2)
{
_mzid.DataCollection.AnalysisData.ProteinDetectionList.ProteinAmbiguityGroup[group_id].ProteinDetectionHypothesis[pag_protein_index].PeptideHypothesis[peptide_id].SpectrumIdentificationItemRef[i] = new mzIdentML110.Generated.SpectrumIdentificationItemRefType()
{
spectrumIdentificationItem_ref = sii
};
i++;
}
peptide_id++;
}
}
}
pag_protein_index++;
protein_id++;
}
group_id++;
}
}
XmlWriter writer = XmlWriter.Create(outputPath, settings);
_indexedSerializer.Serialize(writer, _mzid);
writer.Close();
}
public void Mzid110Test()
{
XmlSerializer _indexedSerializer = new XmlSerializer(typeof(mzIdentML110.Generated.MzIdentMLType110));
var _mzid = new mzIdentML110.Generated.MzIdentMLType110()
{
DataCollection = new mzIdentML110.Generated.DataCollectionType()
};
_mzid.DataCollection.AnalysisData = new mzIdentML110.Generated.AnalysisDataType()
{
SpectrumIdentificationList = new mzIdentML110.Generated.SpectrumIdentificationListType[1]
};
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0] = new mzIdentML110.Generated.SpectrumIdentificationListType()
{
SpectrumIdentificationResult = new mzIdentML110.Generated.SpectrumIdentificationResultType[1]
};
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0] = new mzIdentML110.Generated.SpectrumIdentificationResultType()
{
spectrumID = "spectrum 2",
SpectrumIdentificationItem = new mzIdentML110.Generated.SpectrumIdentificationItemType[50]
};
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[0] = new mzIdentML110.Generated.SpectrumIdentificationItemType()
{
experimentalMassToCharge = 1134.2609130203 + 0.000001 * 1134.2609130203 + 0.000001,
calculatedMassToCharge = 1134.26091302033,
calculatedMassToChargeSpecified = true,
chargeState = 3,
cvParam = new mzIdentML110.Generated.CVParamType[1]
{
new mzIdentML110.Generated.CVParamType()
{
accession = "MS:1002354",
value = "0.05"
}
}
};
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[1] = new mzIdentML110.Generated.SpectrumIdentificationItemType();
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[0].Fragmentation = new mzIdentML110.Generated.IonTypeType[1];
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[0].Fragmentation[0] = new mzIdentML110.Generated.IonTypeType()
{
FragmentArray = new mzIdentML110.Generated.FragmentArrayType[1]
};
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[0].Fragmentation[0].FragmentArray[0] = new mzIdentML110.Generated.FragmentArrayType()
{
values = new float[3] {
200, 300, 400
}
};
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[0].PeptideEvidenceRef = new mzIdentML110.Generated.PeptideEvidenceRefType[1];
_mzid.DataCollection.AnalysisData.SpectrumIdentificationList[0].SpectrumIdentificationResult[0].SpectrumIdentificationItem[0].PeptideEvidenceRef[0] = new mzIdentML110.Generated.PeptideEvidenceRefType()
{
peptideEvidence_ref = "PE_1"
};
_mzid.DataCollection.Inputs = new mzIdentML110.Generated.InputsType()
{
SpectraData = new mzIdentML110.Generated.SpectraDataType[1]
};
_mzid.DataCollection.Inputs.SpectraData[0] = new mzIdentML110.Generated.SpectraDataType()
{
FileFormat = new mzIdentML110.Generated.FileFormatType()
};
_mzid.DataCollection.Inputs.SpectraData[0].FileFormat.cvParam = new mzIdentML110.Generated.CVParamType()
{
name = "mzML format"
};
_mzid.SequenceCollection = new mzIdentML110.Generated.SequenceCollectionType()
{
PeptideEvidence = new mzIdentML110.Generated.PeptideEvidenceType[1]
};
_mzid.SequenceCollection.PeptideEvidence[0] = new mzIdentML110.Generated.PeptideEvidenceType()
{
endSpecified = true,
startSpecified = true,
isDecoy = false,
start = 2,
end = 34,
dBSequence_ref = "DB_1",
peptide_ref = "P_1",
id = "PE_1",
};
_mzid.SequenceCollection.Peptide = new mzIdentML110.Generated.PeptideType[1];
_mzid.SequenceCollection.Peptide[0] = new mzIdentML110.Generated.PeptideType()
{
id = "P_1",
PeptideSequence = "GPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILR",
Modification = new mzIdentML110.Generated.ModificationType[1]
};
_mzid.SequenceCollection.DBSequence = new mzIdentML110.Generated.DBSequenceType[1];
_mzid.SequenceCollection.DBSequence[0] = new mzIdentML110.Generated.DBSequenceType()
{
id = "DB_1",
name = "Protein name",
accession = "ACCESSION",
};
_mzid.SequenceCollection.Peptide[0].Modification[0] = new mzIdentML110.Generated.ModificationType()
{
locationSpecified = true,
location = 17,
monoisotopicMassDeltaSpecified = true,
monoisotopicMassDelta = 57.02146373,
cvParam = new mzIdentML110.Generated.CVParamType[1]
};
_mzid.SequenceCollection.Peptide[0].Modification[0].cvParam[0] = new mzIdentML110.Generated.CVParamType()
{
accession = "MS:1001460",
name = "unknown modification",
value = "Carbamidomethyl",
cvRef = "PSI-MS"
};
_mzid.AnalysisProtocolCollection = new mzIdentML110.Generated.AnalysisProtocolCollectionType()
{
SpectrumIdentificationProtocol = new mzIdentML110.Generated.SpectrumIdentificationProtocolType[1]
};
_mzid.AnalysisProtocolCollection.SpectrumIdentificationProtocol[0] = new mzIdentML110.Generated.SpectrumIdentificationProtocolType()
{
ParentTolerance = new mzIdentML110.Generated.CVParamType[1]
};
_mzid.AnalysisProtocolCollection.SpectrumIdentificationProtocol[0].ParentTolerance[0] = new mzIdentML110.Generated.CVParamType()
{
unitName = "dalton",
value = "0.1"
};
_mzid.AnalysisProtocolCollection.SpectrumIdentificationProtocol[0].FragmentTolerance = new mzIdentML110.Generated.CVParamType[1];
_mzid.AnalysisProtocolCollection.SpectrumIdentificationProtocol[0].FragmentTolerance[0] = new mzIdentML110.Generated.CVParamType()
{
unitName = "dalton",
value = "0.01"
};
TextWriter writer = new StreamWriter("myIdentifications.mzid");
_indexedSerializer.Serialize(writer, _mzid);
writer.Close();
var identifications = new MzidIdentifications("myIdentifications.mzid");
Assert.AreEqual(1134.26091302033, identifications.CalculatedMassToCharge(0, 0));
Assert.AreEqual(3, identifications.ChargeState(0, 0));
Assert.AreEqual(1, identifications.Count);
Assert.AreEqual(1134.26091302033 + 0.000001 * 1134.2609130203 + 0.000001, identifications.ExperimentalMassToCharge(0, 0), 1e-10);
Assert.IsFalse(identifications.IsDecoy(0, 0));
Assert.AreEqual("MS:1001460", identifications.ModificationAcession(0, 0, 0));
Assert.AreEqual("PSI-MS", identifications.ModificationDictionary(0, 0, 0));
Assert.AreEqual("Carbamidomethyl", identifications.ModificationValue(0, 0, 0));
Assert.AreEqual(17, identifications.ModificationLocation(0, 0, 0));
Assert.AreEqual(57.02146373, identifications.ModificationMass(0, 0, 0));
Assert.AreEqual("spectrum 2", identifications.Ms2SpectrumID(0));
Assert.AreEqual(1, identifications.NumModifications(0, 0));
Assert.AreEqual("GPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILR", identifications.PeptideSequenceWithoutModifications(0, 0));
Assert.AreEqual(0.1, identifications.ParentTolerance.Value);
Assert.AreEqual(0.01, identifications.FragmentTolerance.Value);
Assert.AreEqual(.05, identifications.QValue(0, 0));
Assert.AreEqual("Protein name", identifications.ProteinFullName(0, 0));
Assert.AreEqual("ACCESSION", identifications.ProteinAccession(0, 0));
Assert.AreEqual(new float[3] {
200, 300, 400
}, identifications.MatchedIons(0, 0, 0));
Assert.AreEqual(3, identifications.MatchedIonCounts(0, 0, 0));
Assert.AreEqual("2", identifications.StartResidueInProtein(0, 0));
Assert.AreEqual("34", identifications.EndResidueInProtein(0, 0));
Assert.AreEqual(2, identifications.NumPSMsFromScan(0));
}
